Command Line Interface

crema version 0.0.9.dev8+ga8f8065

Written by Andy Lin, Donavan See (seed99@cs.washington.edu), and William E Fondrie (wfondrie@uw.edu) in the Department of Genome Sciences at the University of Washington

Official code website: https://github.com/Noble-Lab/crema

More documentation and examples: https://crema-ms.readthedocs.io/

usage: crema [-h] [-s SCORE [SCORE ...]] [-f FILE_ROOT] [-o OUTPUT_DIR]
             [-e EVAL_FDR] [-m {tdc}] [-p {psm-only,peptide-only,psm-peptide}]
             [-r {best,combine}]
             psm_files [psm_files ...]

Positional Arguments

psm_files

One or more collection of peptide-spectrum matches (PSMs) in the mzTab or Tide tab-delimited formats.

Named Arguments

-s, --score

One or more columns that indicate possible scores by which to rank the PSMs. If more than one is provided, the best will be selected automatically. If none are provided, crema will try all available scores.

-f, --file_root

This string will be added as a prefix to all output file names.

-o, --output_dir

The directory where output files will be created. Defaults to the current working directory.

-e, --eval_fdr

The FDR threshold by which to choose the best score column and to report in logging messages.

Default: 0.01

-m, --method

Possible choices: tdc

The confidence estimation method to use.

Default: “tdc”

-p, --pep_fdr_type

Possible choices: psm-only, peptide-only, psm-peptide

The peptide-level FDR estimation method to use.

Default: “psm-only”

-r, --prot_fdr_type

Possible choices: best, combine

The protein-level FDR estimation method to use.

Default: “best”

Output

Crema will produce three output files:

  1. A text file named “crema.psms.txt” containing an additional column (crema q-value) of PSM-level confidence estimate results appended to the spectrum, peptide, and score columns from the input file.

  2. A text file named “crema.peptides.txt” containing an additional column (crema q-value) of peptide-level confidence estimate results appended to the spectrum, peptide, and score columns from the input file.

#. A text file named “crema.proteins.txt” containing an additional column (crema q-value) of protein-level confidence estimate results appended to the protein ID and score columns from the input file.

  1. A text file named “crema.log.txt” containing the logging information from using crema. Note that this file is only created when running crema through via the command line.

Note that the program writes to the current working directory by default.

  • The name of the output directory can be specified using the —output_dir argument.

  • A prefix can be added to the output file names be using the —file_root argument.